MolNFT v1 · #84510 · protein
LSD1-corest in complex with plsflv peptide
3ZMV · Lysine-specific histone demethylase 1A: “LSD1-corest in complex with plsflv peptide”. X-ray diffraction, 1 ligand (FAD), 12 pockets (best druggability 0.85). MolNFT v1 #84510 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 3ZMV
- Type
- protein
- Length
- 809 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lysine-specific histone demethylase 1A; Rest corepressor 1; Pksflv peptide
- EC
- 1.-.-.-
- UniProt
- O60341, Q9UKL0
- Ligands
- FAD
- Pockets
- 12 · best druggability 0.85
Structure
x-ray diffraction · 4 distinct chains · 47% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lysine-specific histone demethylase 1A (EC 1.-.-.-) | protein | 665 | 44% helix, 16% strand | O60341 |
| B | Rest corepressor 1 | protein | 133 | 63% helix, 0% strand | Q9UKL0 |
| C | Pksflv peptide | protein | 6 | 50% helix, 0% strand | — |
| D | Pksflv peptide | protein | 5 | 0% helix, 20% strand | — |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 350 | 0.85 | 0.94 | 62 | FAD |
| 2 | 375 | 0.63 | 0.78 | 36 | empty |
| 3 | 196 | 0.47 | 0.75 | 22 | empty |
| 4 | 93 | 0.44 | 0.78 | 19 | empty |
| 5 | 133 | 0.40 | 0.74 | 16 | empty |
Interfaces
3 interfaces between chains.
- A–B · 2780 Ų buried · 20 hydrogen bonds · protein-protein
- A–C · 609 Ų buried · 6 hydrogen bonds · protein-protein
- A–D · 344 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt O60341
- Every structure of UniProt Q9UKL0
- Elsewhere: RCSB PDB 3ZMV · PDBe 3ZMV · UniProt O60341 · UniProt Q9UKL0
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